Cellxgene Versions Save

Summary: This release contains bug fixes for a few issues with mismatched colors between the left sidebar and the main canvas (issues #2007 and #2011), and improved error handling for —experimental-annotations-ontology (issue #2024).

Summary: We fixed an issue caused by a h5py major version change. As a result, h5py is now restricted to < 3.0.0

Summary: We fixed an issue where some of the continuous attributes of cell data were not visible in the right hand side bar as well as an issue with experimental re-embeddings failing.

Summary: We fix an issue with colors in the left sidebar not matching the colors in the main canvas area. The Docker contained was updated following a breaking change. We updated the way that static assets are served such that cellxgene can be used behind a proxy. We also corrected an issue with re-embeddings that was broken was small gene counts.

Summary: 0.16.2 corrects a couple of breaking changes from 0.16.0. We fix the bug with gene expression scatterplots where the x and y axes were swapped and we also fix the support of launching cellxgene with the --experimental-enable-reembedding flag.

Summary: 0.16.0 introduced a number of refinements to the cellxgene application. We have added a number of UI enhancements such as histogram coloring, improvements to the differential expression user experience, and re-embeddings. This release also includes a large number of bug fixes and small performance improvements.

We are currently testing an alpha version of a hosted cellxgene at cellxgene.cziscience.com. While it is not yet feature complete, any feedback would be welcome.

Added

• Support for coloring right-side histograms #1218
• Config file that provides the ability to set various parameters of launching cellxgene via either the server or the launch CLI command. #1264
• Tooltip for category names #1278
• Compression of HTTP responses for servers launched via the CLI #1285
• Differential expression UI and config visibility improvements #1336
• Support for user-defined category-label colors #1402
• Added ability to select labels for differential expression instead of only subsets #1494
• Improvement to lasso “can close” visual feedback #1550
• Categorial UI improvements including support for renaming the annotations file #1649, #1660
• Support for re-embedding #1679 - experimental. Functionality may change in the future.

Changed

• Show single value instead of entire histogram if the minimum and the maximum are the same #1554
• Major refactor to use lazy data loading from the server side using react-async #1571

Fixed

• Added a workaround to accommodate a bug in AnnData make_index_unique that does not work under certain conditions. #1260
• Assorted small UI fixes: proper truncation #1320
• Various histogram fixes like x-axis labeling #1363, performance improvement #1390
• Fix for brushing subset of a gene distribution after subsetting data #1409
• Fix to cache crossfilter when embedding type is changed #1493
• De-duping gene sets #1490

Security

• Removed client package that introduced security vulnerabilities #1248

Summary: 0.15 resolves incompatibilities with the current anndata/scanpy releases, improves ontology-driven label input in user annotations, moves annotations to a supported feature, and resolves a number of miscellaneous bugs and UI issues.

Added:

• User annotations feature has moved to a fully supported feature, and is no longer experimental (nb. command line params have changed, and annotations are enabled by default - see documentation for more information).

• Experimental support for ontology-driven annotation/label input was further enhanced. Users can now pick from an ontology or define their own label in a single dialog, and ontologies are available for both label and category creation and editing.

• Code coverage reports added to the github repo CI pipeline

• Significant additions to unit & smoke tests and configuration testing in the CI pipeline

• Added experimental support computed re-embedding on user-selected cell sets.

• Better handling of annotations with very large number of categorical values.

Changed:

• Resolved incompatibility with annata 0.7 and remove pinned Python dependencies for anndata, h5py and tables modules. This resolves several compatibility issues with H5AD files. #1157, #1202

• Reset UI replaced with Subset and Unsubset (#1183), and unsubset no longer deletes genes in the right side bar (fixes #1171).

• Work in preparation for a web-hosted cellxgene (not yet available or complete), including:

  • Incremental loading of data on the front end

  • Refactoring the back-end to support a cloud-native data format built upon tiledb.

  • #1140, #1163, #1200

• Javascript and Python package dependencies updated.

• Variety of small UI improvements throughout the application, including more readable data labels on the main graph (#1141, #1160), better handling of long strings (#1206), improved enable/disable state on buttons, etc.

Fixed:

• Datasets with more than 32 annotations would occasionally cause the crossfilter to get confused, and selection state to be lost (#1162)

• Undo/redo was not working correctly with color-by-annotation and other UI actions (#1165)

Fixed:

• #1137 - labels do not correctly pan/zoom

Summary: 0.14.0 adds ontology-based autosuggestions to the experimental annotation feature, category labeling in the main graph/embedding, and a number of bug fixes and incremental improvements.

Added:

• The experimental annotations feature is augmented with the ability to autosuggest labels from an ontology. Ontology is specified from an .obo file. See the --experimental-annotations-ontology command line flag.
• Main embedding (graph) display enhanced with the ability to display category names over the center of the constituent cells. Enabled/disabled by a new UI button in the button bar.
• When launched, cellxgene will inform users when a new version is available on PyPi.org. This check may be bypassed with the new --no-upgrade-check command line option.

Changed:

• Labels / names in the user interface will now display in a sorted order, including embedding names, annotation names, and categorical annotation values.
• Various internal build updates and improvements.
• Fonts needed by the application are now served by the internal web server, rather than relying on internet connectivity.
• Javascript and Python package dependencies updated.
• FAQ link removed from Info menu
• All large histograms will now have a consistent number of bins (PR #1086)
• User-created annotations may now contain additional characters (now allow alphanumeric, plus -_.() and single spaces. Fixes issue #1113.
• The recent 0.7.* release of the anndata module is incompatible with cellxgene. This release pins the anndata dependency to 0.6.22post1 (the most recent compatible version).

Fixed:

• A significant number of bug fixes to experimental annotations, including #1050, #1057, #1036, #1055 and others.
• Annotation file name, specified by --experimental-annotations-file, will now allow file names containing a hyphen. Fixes issue #1072
• Fixed bug which would cause user-created annotations to lose the (mandatory) unassigned category. Fixes issue #1090
• Various layout and whitespace improvements throughout the app.
• Added missing python requests package to requirements.
• Fixed bug that would crash if the user created an annotation name which was the same as another existing annotation name. Fixes issue #1112
• Ensure that all user-created annotation labels are correctly saved, without transformation, to the annotations CSV file. There were several labels (eg, 'nan') which would not be saved correctly to the annotations CSV file. Fixes issue #1111.
• Some sequences of actions caused the undo button to behave unpredictably. This is fixed by #1099

Summary: 0.13.0 introduces a layout change, moving all continuous data histograms into a dedicated panel: the "right side bar". In addition, 0.13.0 includes significant improvements and bug fixes to the experimental "user annotation" feature.

Added:

• Introduced a "right side bar" containing all continuous metadata and gene expression histograms.
• [Experimental feature, may be incomplete or unstable] Significant improvements to the user annotation functionality, allowing users to annotate groups of cells with categorical metadata:
  • Command line options related to annotation renamed and reorganized -- see cellxgene launch --help for usage.
  • Added simple multi-user support for hosted instances of cellxgene, to avoid the possibility of users over-writing each others’ metadata.
  • Add a provenance header to the annotations output CSV file.
  • Many bug fixes, usability and stability improvements.

Changed:

• Command line option --skip-qc/--run-qc (a toggle) changed to a flag named --skip-qc.
• Command line help (via the --help option) improved.
• Reorganized and improved cellxgene documentation, available at https://chanzuckerberg.github.io/cellxgene/.
• Javascript and Python package dependencies updated.
• Dockerfile now contains python-requests package (#1019).
• Migrate from deprecated Pandas API (#1021).

Fixed:

• Various layout issues resolved throughout app.